DKIM signature verification disabled, corresponding features not available. If not intentional, consider enabling it by setting: $enable_dkim_verification to 1, or explicitly disable it by setting it to 0 to quench down this warning.

ISPConfig has a security mechanism that stops the update in case that the dumped sql database is too small to prevent that the update fauls due to problems with the databse dump. But sometimes this routines is wrong, e.g. if you have fery few records on the slave server.

Please check the file existing_db.sql which has been created in the install folder during the ispconfig update if it seems to contain all data records that you would expect on the server, or if it contains nothing or just a error message.

Locate uses a databse of all system files which gets updated nightly. So the file will show up with locate tomorrow.

Regarding the original issue. Please take a look into the file existing_db.sql with atext editor. Does it look like all your records /sites email user etc) that shall be on this server are listed there?